Hi Aaron,
I am not too sure what is going on here, technically you are correct in the sense that if you choose Method to assign ref numbers, then they should be created in sequence. The only way I can really see this happening is if someone changed the invoice number in QuickBooks, then Method saw this new number and created all future invoices based off this new QB Invoice Number. For me to get a better idea on what is going here, it would help if you could turn on the MethodSupport user and I could login to your Account and look at these transactions in discussion.
You can turn on MethodSupport by going to Customize-Users, locate the MethodSupport User in the second section of this screen and make sure there is a checkmark in the "Active" column. Once you have done this, please privately email me your Method CompanyAccount name, as well as some contact information for you. I can use the Invoice Numbers you mentioned in the above post for examples, however if you have more that you know of, please include these reference numbers in your email also. You can either send me an email through the forums, or to b.citren@methodintegration.com
I will also attempt to recreate this in my own account, but it would help to see yours first to get a sense of your setup.
-Ben